Rhythmic nuclear import mediated by importins regulates the Neurospora circadian clock

Circadian clocks in eukaryotes rely on precisely regulated negative feedback loops to generate daily rhythms. However, the delay mechanisms that extend this structurally simple feedback loop to ∼24 h are not yet fully understood. In the filamentous fungal model organism Neurospora crassa, the negative arm complex, centered by FREQUENCY (FRQ), must enter the nucleus to repress the White Collar Complex (WCC) and close the feedback loop, but the mechanisms and dynamics of its nuclear transport have remained unresolved. Using long-term live-cell imaging and fluorescence recovery after photobleaching, we demonstrate that FRQ nuclear import is an active circadian-regulated process that is fastest early in the subjective day and whose rate progressively decreases as nuclear FRQ approaches peak levels, corresponding to altered direct binding between FRQ and Importin α. We further establish that Importin α is required for the spatial regulation of FRQ and WCC, as well as the correct timing of Neurospora circadian clock, whereas the nuclear accumulation of nonclock-related free White Collar-2 (WC-2) does not require Importin α. Analysis of the three Neurospora Importin β homologs reveals that each of them contributes differently to the circadian clock through pathways beyond FRQ or WCC nuclear import. More specifically, we find a genetic interaction between importin β3 and protein phosphatase-4. Together, these findings indicate that nuclear import is a selective, dynamic, and rate-limiting regulatory step in the fungal circadian clock and reveal both conserved and fungal-specific mechanisms by which importins tune circadian timing.